Remove working documents and backups

Cleaned up temporary files created during project overhaul:
- docs/.analysis/ - migration analysis files (13 files)
- docs/drafts/ - draft documents
- docs/archive/README-backup-2026-01-29.md - backup file
- data/metadata/metadata.json.backup
- src/handlers/api_handler/graph/mod.rs.backup
- prd2build.md, task.md - root working files

Co-Authored-By: claude-flow <ruv@ruv.net>

Author: Roo Code